I don't know why , but if you try to assign some units , there is some problems with other civs . Player 0 will get all but for other players the units are skipped . I've seen in the SDK that's because when the process add initial items , it check if there is already units for the player .
I've also encounter some bug doing that (except with barbarian units) . But i've not try to add some units with the last BtS patch . This bug will perhaps not occur anymore .
The way i use to add some units with my script is to add an event in the event manager , call it during map generation (it's done after onGameStart) and delete the event in CvEventManager when the units are added .
Tcho !